We study genes of the rabbit immune system by techniques of molecular biology and immunology. Alternative mechanisms such as gene conversion (g.c.) appear to contribute to the diversification of the antibody repertoire in the rabbit. The rabbit appendix develops rapidly between birth and 6 weeks of age, when it seems to reach its maximum size. We analyzed diversification from germline VH gene sequence in individual rabbit appendix follicles. Our results suggest that g.c. is occurring to diversify germline gene sequences in the dark zone cells of the appendix follicles of six week old rabbits. Some changes may have been due to either g.c or somatic hypermutation. Earlier, we found that a relatively small deletion of a segment containing 3' VH genes leads to a mutant phenotype in Alicia (ali) rabbits. We found that the products of the first functional VH gene (VH4a2) or VH4a2-like gene(s) were expressed in two to eight-week-old mutant Alicia; expression of a-negative genes was also elevated but the relative proportions of a-negative decreased as the relative levels of expression of the VH4a2 or VH4a2-like gene(s) increased. The appearance of sequences resembling that of the VH1a2 gene which is deleted in the mutants may be due to g. c. that altered the sequence of the rearranged VH4a2; rearrangement of upstream VH1a2-like genes may also occur later in development. We described the rabbit RAG locus and genomic and expressed RAG-1 and RAG-2 genes. Genetic polymorphism of the rabbit RAG-2 gene was observed by sequencing and Southern analyses. Expressed RAG-2 cDNAs with different sequences were both functional in a recombinase assay. RAG-1 and RAG-2 positive cells can be found in the 6 week normal rabbit appendix. Scattered throughout the M cells pockets, the corona, and both the dark and light zones of germinal centers. PCR allows us to specifically identify excision circles resulting from VL to JL DNA rearrangements. Circular products reflecting VLJL rearrangements were detected in the appendix of two week-old and adult animals.